updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

[jalview.git] / src / jalview / schemes / NucleotideColourScheme.java

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index caa6998..e8382d5 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,37 +1,84 @@
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-\r
-public class NucleotideColourScheme extends ResidueColourScheme\r
-{\r
-  public NucleotideColourScheme() {\r
-  super(ResidueProperties.nucleotide,0);\r
-  }\r
-\r
-\r
-  public Color findColour(String n)\r
-  {\r
-    System.out.println("called");\r
-    return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-  }\r
-\r
-\r
-  public Color findColour(String n, int j, Vector aa) {\r
-\r
-    if (threshold == 0 || aboveThreshold(aa, n, j))\r
-      try\r
-      {\r
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        return Color.white;\r
-      }\r
-    else\r
-      return Color.white;\r
-\r
-  }\r
-\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.schemes;
+
+import java.awt.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+    /**
+     * Creates a new NucleotideColourScheme object.
+     */
+    public NucleotideColourScheme()
+    {
+        super(ResidueProperties.nucleotide, 0);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n)
+    {
+        // System.out.println("called"); log.debug
+        return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n, int j)
+    {
+        if ((threshold == 0) || aboveThreshold(n, j))
+        {
+            try
+            {
+                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+            }
+            catch (Exception ex)
+            {
+                return Color.white;
+            }
+        }
+        else
+        {
+            return Color.white;
+        }
+
+        if(conservationColouring)
+         applyConservation(j);
+
+       return currentColour;
+    }
+}